His Father's Son
by irishdragon12000
Summary: This is an attempted AU on season 3 and maybe beyond. I didn't like the entire direction of season 3 and felt that that killed the series. In my opinion the series does not work without Chuck/Sarah so there will not be any manufactured love triangles. Chuck and Sarah are together, but the intersect 2.0 does not have the same effect on Chuck as in the show
1. Chapter 1

_A/N: I don't own Chuck nor make any $ from it_

Prologue

A warm summer rain softly began to fall as a beautiful young woman leafed through a file, while sitting in her fancy German car. She looked right out of central casting as a movie star, with her athletic figure, beautiful blonde hair and blue eyes. The eyes however were not bright and warm; they were cold and detached. She was an amalgam of different people, killer, lover, savior and nightmare; all carefully manufactured for a specific situation. She was a young woman of 26 but had already lived several different lives. She had killed 12 men in her young life, and even though they were evil, she surrendered a part of herself to each one. Not her manufactured self, but who she was before, her true self. Over time it got easier for her to forget who she was, as the pain of realizing who she became was too great to bear.

She was tired, more tired they any 26 year old should be. All she knew anymore was her mission, and as she read the name in her file again, her mission was a man named Bartowski. He was an underachiever, but appeared to have a very high IQ, and was very good with computers. His best friend apparently screwed him over in college and it seemed to affect him, possibly contributing to his current malaise. Although she had memorized the file, she found herself looking at it for the eighth time, or rather staring at the picture in the file. She got a strange feeling when she looked at him and responded in a very unusual way for her, she smiled. A real genuine smile, something she had not done since before she lost herself.

 _Why am I acting like this? His picture looks like a bad prom picture_

she thought.

Then she did the last thing she ever expected, she giggled.

 _Snap out of it! Focus! Clear the mechanism_ …a voice inside her head said.

With one final look at the file, she got out of her car and entered the store.

The beautiful blonde walked inside and quickly surveyed the room. She spotted her quarry in the back at the desk helping many frantic people with their computer problems. He looked rather sloppy with unruly hair, a loose fitting white button down shirt, black pants and sneakers. Her experience told her that threat level cannot be quantitated based on appearance of the mark, but there was something about this man that was different.

 _He doesn't look like a threat…God who even wears those sneakers anymore,_ she thought to herself as she surveyed him.

She could hear him frantically talking to people and involuntarily smiled at his quick speech pattern and wild gestures.

She quickly steeled herself from her thoughts as she refocused on her mission. Identify Bartowski _. Make contact. Use the name Sarah for mission. Assess the situation. Retrieve information. Terminate if necessary._

She took a deep breath and approached the mark.


	2. Chapter 2

_A/N: I don't own Chuck nor make any $ from it_

General Diane Beckman looked through the file on her desk and then at the man seated across her desk trying to read any perceptible trait of uncertainty. Satisfied that his report was accurate she closed the file and began to wonder how this could have happened. The previous 96 hours had been a nightmare. A major security penetration at the NSA by an unknown external entity revealed that the deputy director, a man named Neil Lomax was compromised, and the intersect project as well. Beckman knew about Lomax, who was now a fugitive having escaped before the net fell, but now she knew who compromised the intersect project, a junior agent named Daniel Shaw.

"So this Daniel Shaw uploaded a virus into the newest intersect," she glared at the man.

"I am sorry Ma'am. It appears that the virus was uploaded during the final beta test and remained dormant. It was not detected on diagnostics because it wasn't active. We believe that it was initiated during Agent Bartowskis first flash, possibly triggered by the increased neural synapse activity," the man replied.

" We knew that there was something wrong with Agent Bartowski, in particular the severity of his flashes, but we had direct orders from former deputy director Lomax to keep it confidential. I did not want to come to you until I had absolute proof and I needed to trace everything back to Shaw," the man replied.

Jack Reber was a 40-year veteran of "inside the beltway" life and was one of the original intersect support team that had worked with Steven Bartowski.

"What are the effects of this virus Dr. Reber?"

"Well Ma'am it's a complicated issue."

"How so?"

"Well technically Agent Bartowski should be dead by now."

"Excuse me?"

"Allow me to explain Ma'am" Reber said as he went into an explanation of what the intersect team theorized was going on with Chuck's health as well as new potential developments that sounded like pure science fiction.

Beckman was stunned by the explanation and barely realized that 2 hours had passed before Reber stopped talking.

"How is that even possible," she asked in a bewildered tone.

"At this point Ma'am we don't really know. All I can tell you is that Mr. Bartowski's brain is very unique" Reber replied.

"I don't doubt it," Beckman said with a sly smile on her face.

"So you do not believe that the intersect is causing Bartowski any harm," she queried.

"No Ma'am. As a matter of fact it is keeping him alive."

Beckman moved her eyes down to a picture on her desk of two young female Air Force lieutenants graduating from the academy, and slowly shook her head. _How much does one family have to give_ she thought, as she brought her attention back to Reber.

"In regards to the other new developments that you mentioned; how will this affect him," Beckman asked.

"Well Ma'am if it means what we think it means, we might be seeing the next step in human evolution," he replied soberly.


	3. Chapter 3

_A/N: I don't own Chuck nor make any $ from it_

This was not how it was supposed to be for Chuck Bartowski as he lay in bed with his eyes closed after suffering another massive headache. It was Valentines Day and he was going to take his beautiful girlfriend out for a real date. No missions, no more cover relationships, just the two of them in love and happy.

"Sarah I'm so sorry about tonight. I really wanted our first real valentines day to be special and I just blew it," he said dejectedly.

"Don't worry Chuck. You didn't blow anything," Sarah replied as she gently ran her fingers through his hair.

"Hey at least my nose didn't bleed today so that's something," he said as he cracked a wide smile.

"That's true," she replied.

Sarah was trying to keep calm but the concern was evident on her face. Ever since Chuck had downloaded this new intersect he had been suffering from massive headaches and occasional nosebleeds, which were becoming all too frequent for Sarah's liking. She could tell that this new intersect was different from the last one by how frequently he would flash, and how physically taxing the flashes were on him. He would coil up like a spring when he flashed now and sometimes became physically ill after having one.

Despite these episodes there were major benefits as well. Chuck seemed to have an almost superhuman capacity to merge information and make connections based on seemingly immaterial events. The last few months they had eradicated Fulcrum, and were well on their way to the Ring as well. Indeed team intersect was a weapon of superior means against any foe that the country encountered. This new status allowed them special dispensations, including Chuck and Sarah free to pursue a true relationship, and Casey now in command of a 20-man strike force.

Sarah's mission had evolved as well. Professionally, she was now his partner rather than his handler, but her primary goal was still his protection. Personally she was that happiest that she had ever been. No one had ever been able to understand her or reach her the way that he had been able to, and no one could slay the demons that haunted her until Chuck. He gave her a gift that comes from being loved unconditionally; he made her a better person.

He filled the void in her soul and gave her access to a life of happiness, a life that previously had been beyond her wildest dreams. No longer was she so angry at life or frustrated with the universe, her life and universe finally made sense. She loved him with every ounce of her soul and wanted to spend the rest of her life with him. She was fiercely protective of Chuck on missions even before she realized that she loved him, but now she became his own personal guardian angel, ready to destroy any threat to him.

"Chuck I'm worried that these episodes are getting out of control. I know you don't want me to tell Beckman, but I think we should at least tell your sister," Sarah said.

"Sarah it's nothing major. Besides Ellie and Devon are too busy with their new jobs in Boston. I don't want to concern her over nothing," he replied.

"It's hardly nothing! Chuck you have been getting worse! These new flashes you are having are dangerous, I see what they do to you. I want you checked out" she demanded, the emotion evident in her voice.

He opened his eyes and looked at her beautiful face full of concern and worry. He never imagined in a million years that he would ever find someone so incredible as Sarah Walker. She was so beautiful and amazing that he nearly lost himself every time he looked at her. The episodes were getting worse and he knew it as well as Sarah did; however he didn't want to cause her anymore worry. 5 months ago he probably would have tried to bluff his way out of this, but two new realities were making that impossible right now. The first was that he was deeply in love with her and he knew that he had a responsibility to her to take care of this and put her fears to rest. The second reality was that she was one of the most dangerous assassins in the world and had a very short fuse. A pissed off girlfriend is one thing, but a pissed off assassin is an entirely different animal.

"Okay Sarah, we will tell the General. I will get checked out," he smiled to her.

"I'll go over to Casey's and conference her now," Sarah said visibly relieved as she kissed him lightly on the lips before leaving to get her phone and call it in.

Had she stayed a few more seconds her relief would have turned to shock as Chuck closed his eyes seemingly struggling to reach for a glass of water on the end table, until the glass appeared to magically slide into his hand.


	4. Chapter 4

_A/N: I don't own Chuck nor make any $ from it_

"Agent Walker has Agent Bartowski flashed on something," the two dimensional face of General Beckman said through John Casey's television.

"No General he didn't, but we have a situation that we need to discus in regards to Chuck's health," Sarah replied.

"For the better part of the last 2 months Chuck has been getting severe headaches and nosebleeds. The headaches have been getting progressively worse to the point of almost incapacitating him. They seem to have been triggered by his flashes at first, but now they are more frequent," Sarah continued.

"I see and what about the nosebleeds," Beckman countered.

"Well Ma'am they seem to have gotten less frequent," Sarah replied.

"Major Casey your assessment please," the General said as she looked at the ramrod figure of John Casey standing next to Sarah.

"Well Ma'am I would concur with Agent Walker's assessment of the situation. Although I don't have the same level of access to Agent Bartowski as she does, when I have seen him flash, he does display those behaviors," he smirked while looking at Sarah.

Sarah rolled her eyes at the comment.

"The electronic biosensors that Bartowski was fitted with last month have shown a increase lactic acid which suggests that less oxygen is getting into his blood, particularly around the time of the flashes. I have sent these findings to medical and they have confirmed with their remote monitoring. However they have said this is inconclusive," Casey said.

The general looked pensive as she thoughtfully scratched her chin. She knew about the lactic acid build up and she knew that her agents would find out everything she knew eventually, but she wanted to hold out on telling them a little longer.

"Major in your professional opinion have these headaches affected Agent Bartowski's operational competence," Beckman said.

"As of yet No Ma'am. Agent Bartowski has always been able to operate during missions. That being said I would suggest that we have him checked out before our next field operation. I do believe that he needs a medical evaluation," Casey said as he shifted his eyes to Sarah.

He could see the veins on the side of Sarah's neck start to bulge and he knew that she was annoyed that Beckman had asked him first and not her. Beckman was as "by the book " as it gets and Sarah's emotional attachment to Chuck could invalidate her assessment of Chuck's competence right now.

"Agent Walker do you agree with the Majors assessment," Beckman asked Sarah.

"I do. Chuck is responding worse to the flashes then ever before and his headaches are more frequent. We don't know when he will flash, and as the headaches are getting progressively worse keeping him in the field is too dangerous," Sarah replied.

 _That damn light!_

Chuck thought to himself as he angrily rolled on the bed. He wanted to turn it off, but as soon as he opened his eyes to get up the effect of the light made his headache feel 5 times worse.

He felt the flash begin to materialize, but unlike a typical flash, this one seemed to govern his mind and control his thoughts. The flash completely took control over his mind to such an extent that he was consciously unaware of what was happening. He thought about his pain and what was the source of it and a picture of the lamp materialized in his mind, it looked like his normal lamp with one exception. He could actually see a thin line of little brightly lit particles flowing through the lamp and radiating off the bulb.

He focused in on the stream and suddenly the stream was moving so fast that he no longer saw the individual particles, but just a solid line moving through the lamp. He could see now that the brightly lit particles that were radiating off the bulb before, were now pulsating off with such force that the light bulb seemed to be stretching.

Suddenly there was a loud crack, which fried every electrical device in his bedroom and plunged his room into darkness. The flash released him and he became aware that the light was off.

"Thank God," he sighed, as he suddenly felt very tired and promptly fell asleep

The General looked thoughtfully at the screen for a few seconds after taking the comments of her two agents.

"Very well as you two are in agreement…" she began when she was suddenly interrupted by Chuck's biometric alarm, which sounded on Sarah's phone and Casey's computer.

"I've lost video feed….. surveillance is down," Casey yelled to an already running Sarah.

"Chuck! Chuck," Sarah screamed as she burst through their front door running directly for their darkened bedroom with her gun drawn.

"Oh my God Chuck," Sarah screamed with fear she saw him in their bed and rushed up to him.

"Jesus Sarah! What," Chuck said as he was suddenly shocked out of his sleep by the screams and the feel of her body collapsing on top of his.

"Chuck! Are you OK," Sarah asked flooded with relief at hearing his voice and feeling him move beneath her.

"Sarah what's wrong? I'm ok…I'm ok…what is going on…. are you hurt," he asked her with fear and confusion in his eyes.

"Oh God Chuck! Your Biometric went off. I thought you were…I thought that…somebody got you…I..," she stammered.

"We thought you were dead Bartowski. The surveillance is down and what the hell happened to the light, there is broken glass all over here," Casey answered as he quickly called the general updating her on the situation.

"You thought I was dead," Chuck said with a smirk and more then a little confused at the recent development.

"Its not funny. I thought with your headaches and the surveillance out…maybe somebody came to get you," Sarah yelled as she burrowed her head into his chest and squeezed him like an anaconda.

Chuck softly stroked her hair and whispered into her ear assuring her that he was ok. He was just about to mention to her that she was going to cut off his airflow when he noticed Casey finish up his phone call with the general.

"Ok you two listen up. Bartowski you have medical at 0600 hrs. The evaluation will last all day and you are not to eat anything from now until testing. Agent Walker I assume that you will police that activity for Bartowski," Casey said with the slightest hint of sarcasm.

"Uh HUH" was Sarah's muffled reply as she kept her iron lock on Chuck.

"Very well then. See you kids bright and early," Casey said as he left their room and closed the front door of the apartment behind him.

Chuck could feel Sarah's grip begin to subside after a few more minutes, and he felt her breathing become more relaxed. After a few more minutes he though she was asleep and slowly tried to maneuver himself out from under her.

"What do you think you are doing," she asked while keeping her head securely on his chest and her eyes closed.

"Oh Sarah I thought you might have fallen asleep… I just wanted to go to the bathroom real quick," he said. He also desperately wanted to escape from her iron grasp and be able to take a full breath for a few seconds.

"Two minutes," she replied as she released him and he got up from the bed.

"Sarah is this really…"

"You now have less then 2 minutes," she replied as she looked at him with her agent eyes, which always gave him a little intimidation.

"Ok," Chuck replied as he made his way to the bathroom.

She quickly locked up the apartment and had just finished changing into one of his shirts when he got back.

"Get into bed Chuck you need your rest."

"Sarah its only 9 pm don't you think you are being a little…"

"A little what Chuck," Sarah said as she went to put her gun in the gun-safe that was built into the end table.

"Oh…nothing…um…you're right," he stammered.

"Get into bed now Chuck," she said with a bit more bite this time.

Chuck hopped into the bed and got under the covers. The room was still in darkness, but he felt her return to her previous position directly on top of him and began to feel her anaconda squeeze.

"Ah man," he said under his breath as he felt her squeeze ever increasing its force.

"What was that," she said.

"Yes Ma'am," he replied as he surrendered to his situation.

"Chuck?"

"Yeah Sarah,"

"What the hell happened to the lights?"


	5. Chapter 5

_A/N: I don't own Chuck nor make any $ from it_

The secure CIA medical facility looked like any other urgent care facility that seem to proliferate the medical industry nowadays Chuck thought as he walked in with Casey and Sarah. The only two notable differences were the lack of other patients, and the elevator, which took them several stories below ground, revealing a first class facility.

Over the next few hours Chuck was subjected to a multitude of tests to determine what exactly was happening with his health. The final series of tests required sedation and Sarah stayed by his side throughout the entire day, leaving only when she was assured the tests were over and Chuck was moved into the recovery room. She kissed him softly on the forehead as he was wheeled in and made her way up to a private conference room to attend a scheduled briefing with the General. As Sarah opened the door she was shocked to see the General herself standing in front of a digital screen along with Casey, and a pudgy little man in a lab coat who she didn't know.

"Agent Walker please come in," the general said as Sarah closed the door.

"How is Agent Bartowski doing?"

"Well he has been sedated Ma'am. These last few tests were pretty intense on him, but the doctors assure me that he will wake up in a couple hours," Sarah replied a little weary and emotionally exhausted.

"Agent Walker I would like to introduce Dr. Jack Reber, the chief scientist of the Intersect program."

"A pleasure to finally meet you Agent Walker. I have heard many good things," Reber said as he offered her a slightly sweaty hand.

"Thank you doctor. So do you know what is happening to Chuck," she asked.

"Well yes and no," Reber replied looking at the general pensively.

"I'm not sure I understand," Sarah said with the look of confusion on her face.

"Agent Walker. It seems the situation is rather complicated," Beckman answered.

"Please be seated while we explain what is going on Sarah."

A non-descript trash truck stopped at the gate to the alley behind the secure medical center and waited for a guard to allow then through. The guard quickly scanned the badge id of the of the driver and, noticing nothing out of the ordinary, let them through. The truck then made its way to the front of a freight elevator and stopped before the driver turned off the engine and removed his phone.

"We are in position," Daniel Shaw said.

A large man with grey hair and a white beard looked at the image of Chuck Bartowski sleeping soundly in his hospital bed on a high definition monitor. He was tapped into all the surveillance at the hospital as well as castle.

"So easy …never think that anyone could hack their systems," he said as he smiled at the screen.

"The operation is a go. I will override security and unlock the doors," the man said as he quickly skimmed the schematics of the secure medical facility.

He was amazed by the typical mistakes that the government always seems to make when they design secure facilities. They are designed to be almost impenetrable to attack from the outside, but rather simple to assault from the inside. The design of the facility had the recovery room located in the lowest level, which ironically was the least secure of all the levels. The position of the room was located directly next to waste disposal room, which used an unsecured freight elevator to bring up the buildings dumpster for trash removal.

"Go now," he said as he tapped a keyboard overriding all security measures and activating the freight elevator.

Shaw and his men descended in the elevator with an empty trash barrel and quickly made their way out of the waste disposal room. The security in the recovery room was non-existent and Shaw marveled at how the government could be so lax. All that remained between him and Chuck was a small monitoring team of nurses and doctors. Shaw and his men moved in stealthily, their silenced pistols in their hands and quickly eliminated the threat. They dragged the bodies to the waste disposal room and put them inside of one of the facilities dumpsters.

Returning to the recovery room they disconnected Chuck from his IV and heart monitor, while silencing the alarms. They wrapped him up in his sheet and efficiently transferred him into the trash barrel and hit the elevator button raising them back up to the surface. Shaw and his team carried Chuck to the back of the truck and placed the barrel inside a specially designed holding compartment, before lifting up the dumpster with the assassinated medical team, and dumping it into the back of the truck. As they made their way out of the facility Shaw looked at his watch and smirked as he realized the entire operation took just over 9 minutes.


	6. Chapter 6

_A/N For my fellow Physics lovers out there I modified and simplified the UFT to fit the story...The story is fiction I know the UTF is not really as simple as I present it, but I wanted it to fit..please forgive..also_ _I don't own Chuck nor make any $ from it_

It unnerved her when Beckman called her Sarah, and she suddenly felt the tinge of fear when the General pushed a button and the screen came on.

"This man is Agent Daniel Shaw. We believe he is a deep cover operative working for former deputy director Lomax. Shaw had successfully penetrated the CIA and was assigned as a technical analyst to the Intersect project. We believe that he implanted a virus into the new version of the intersect, which we know believe to be causing the headaches that Chuck is experiencing."

"Do we know where he is now General," Casey asked.

"No Shaw is in the wind, but we are actively searching for him," Beckman replied.

"General the virus? What is it doing to Chuck," Sarah asked softly.

"Dr. Reber," Beckman motioned for the little man to take over the briefing.

"Well the virus functions when the intersect is activated and puts an enormous amount of stress on the brain, which in a normal human brain would cause serious issues," he began.

"What kind of issues," Sarah said cautiously.

"We have a theory and I will try to explain it to you, but I don't really understand it all myself," He said as he smiled.

"Based on Chucks previous success with the Intersect, we ran some simulations and made some interesting discoveries about Agent Bartowski's brain," he said.

"What kind of discoveries," Sarah asked as she felt her heart begin to beat rapidly.

"We believe that Agent Bartowski's brain has been able to use the intersect to reorganize, streamline and enhance his mental faculties," Reber replied.

"What do you mean, he got smarter," Casey asked.

"Not really smarter. It's like his brain is more in tune to things," Reber said.

"I'm not following you doctor," Sarah replied.

"Yes I'm sorry its difficult to explain, but we believe that Chuck's brain with the use of the intersect is able to detect the unified field," Reber said.

"The unified field," Casey questioned.

"Tell me Agents have you hear of the unified field theory," Reber asked.

They both shook their heads at his question.

"Well its difficult to explain but it is a theory, coined by Einstein, of tying together electromagnetic and gravitational forces in the universe to explain the nature and behavior of all matter and energy in existence, into a single field" he said.

"A field," Casey asked.

"Yes when talking in terms of physics, a field is just an area under the influence of some force, such as gravity or electricity," he continued.

Both Casey and Sarah looked on dubiously as Reber continued his lecture.

" If someone were able to detect the unified field, well one could potentially control the fundamental forces of the universe. Giving them amazing abilities," he said.

"Such as," Casey asked suspiciously.

"Well for instance the ability for extrasensory perception, or even being able to manipulate matter," Reber said.

"Manipulate matter," Sarah asked

"In basic terms everything in the universe is composed of tiny particles of matter. Even atoms themselves are composed of these particles. These particles, and all molecules that they compose vibrate in what we call harmonic oscillation, sort of like a spring. The vibrations of all these molecules happen at a specific frequency, and they vibrate and stretch at a specific speed. Now imagine if you could control this frequency, then you would be able to manipulate these particles and possibly change the composition of the specific matter," Reber said.

"I'm not following you doctor," Sarah said with a bit more frustration in her voice.

"Ok let me explain," Reber said as he picked up quarter.

"So here I have a quarter and this quarter is composed of tiny particles of matter and that matter is arranged in some exact way to make this quarter which occupies this space here," he began.

"Now imagine that we tap into the frequency of all the molecules that compose this quarter, and I speed up their vibration or I alter the way that they are stretching. I can alter them in such a way that I rearrange the matter that is currently making up this quarter a way that they now no longer make a quarter. For example, lets say I arrange the molecules in such a way to make nitrogen gas. Now since matter cannot be created nor destroyed, it must be conserved and therefore transferred, so the quarter must exist someplace."

" In essence I can transport the matter that is the quarter across space and time to a region where it does not exist and rearrange those molecules that are there in such a way to reform the quarter," Reber said.

What the hell is he talking about," Casey snapped.

"What I am saying Agent Casey," Reber began as he looked at Casey.

"Is that it is possible to teleport matter."

"I'm sorry Dr. Reber, but how does this relate to Chuck," Sarah asked with more then a little frustration now clearly in her voice.

"Please watch this video. It has been shot over the last 2 months," he said.

Sarah and Casey were mesmerized as the video showed various examples of Chuck seeming to move things magically. It also became clearly evident that Chuck was unaware that he was even doing it. He would reach for something that he was unaware was out of his grasp, and it seemed to slide directly to him. Most examples seemed to be when Chuck was alone and under an amount of stress like during his headaches.

"What the hell is going on? What have you done to him," Sarah yelled the emotion evident in her voice.

"Agent Walker please calm down. We have not done anything to him. This is all do to the cognitive ability of Mr. Bartowski, and the function of the Intersect. In seems that stress is an effective trigger to these abilities. It seems it is also the thing that is keeping him alive."

"What do you mean," Casey said.

""The effect of the virus would cause any normal person to have a stroke, or maybe even die. However, the mind has an incredible self-preservation capability, and we believe these new developments are actually giving Chuck the involuntarily ability to heal himself. In essence the intersect found the code written in his brain and amplified it and used it to actually heal his brain. His brain is perfectly healthy," Reber said as he showed them Chuck's brain scans.

Sarah looked at Reber and then down at her hands, her fingers lightly tracing the charm bracelet that Chuck gave her and trying desperately to make sense of the situation. All Chuck ever wanted was a normal life and now this. Her heart was breaking with what they had done to him, what she had done to him. All she wanted to do was get him home and hold him tight.

"Doctor what does this mean for Chuck in terms of his safety..."

She was cut off by the sounds of alarms indicating a breach in security at the lower level and her heart sank when she realized it was the recovery room. She was out the door in an instant with Casey two steps behind her as Beckman grabbed her phone shouting orders for support teams.

Sarah raced through the lower level and stopped suddenly at the blood spatter near the nurses' station. She felt her knees weaken and she began to shake when she saw a blood trail lead from the nurse's station to the waste disposal room.

"Walker wait here," Casey said not wanting to subject her to the possible site of a dead Chuck, as he drew his gun and followed the trail.

Casey braced himself as he reached the door and realized that he wasn't ready to see the site either. He quickly forced the door and was more then a little relieved at the site on the empty waste disposal room.

"Casey," Sarah pleaded crying as he came back to her.

"Chuck is not in there Sarah. He has been taken."


	7. Chapter 7

_A/N: Thanks for the reviews everyone. This goes without saying but I don't own Chuck or make any profit or $ from it_

His eyes fluttered and for a brief second he saw a face and piercing white light, but just as soon his eyes closed and he was back in the void between conciseness and slumber. His body ached all over and his limbs felt like they were made of stone as he became closer to functioning, but he also became aware of a new sensation as well. He could feel five distinct shivers that seemed to originate from five different places in front of him. He could feel two coming from the right side of the room, one from directly in front of him, and two from the left side.

"Are you awake," Chuck heard a voice call to him.

Slowly chuck opened his eyes and focused in on a large man with a large grey beard and thick silver hair. He shook violently and his eyes rolled in his head as images of the man and his family cascaded through his mind. The violence of the flash immediately brought about an excruciating headache, but thankfully no nausea or nosebleed.

"Welcome Mr. Bartowski. Tell me do you know who I am" the man asked with a pleasant expression on his face.

"Well now that you mention it you do look a bit like Kenny Rogers," Chuck replied.

The man remained quiet for a second and then broke out in a booming laugh.

"I can see that your sense of humor is something you get from your father," the large man laughed.

"My Father? How do you…."

"Oh I know all about your father Mr. Bartowski. I know more about him then you probably do," the man said.

"I am very sorry for what is about to happen to you," the man said as he slipped a knife out from his pocket and sliced it down Chucks face.

Chuck shrieked as the blade carved down following around his jaw line, and opening a 5-inch bloody valley down his face.

"I don't like to be lied to Mr. Bartowski, or should I call you Chuck. I know that you are the intersect, and I know that I am in the intersect. Now will you tell me who I am or shall I try the other side of your face," he said as he brandished his weapon menacingly.

"You are Gordon Hertz. Principal programmer of generation one intersect, former East German reach scientist extracted from East Berlin in 1979. By agent codename Frost" Chuck finally admitted.

"Very Good Chuck," Hertz said as he put the knife down on a nearby table.

"What do you want? Why are you doing this to me? People will come for me," Chuck began.

"No one is coming for you Chuck. Your Handlers have no idea where to even begin to search. Look at the hardware around us," Hertz said as he swung his hand around the room.

Chuck looked around the room and saw 6 different workstations and one centralized control station. There were also numerous processors that looked to be daisy chained to one another on the other side of the room. Above him was a camera that he guessed to be recording everything, and over on the left side of the room was a bank of monitors showing the interior of Castle, and every video feed from Casey's surveillance.

"Do you think just anyone could extract you from a CIA secure facility and under the nose of your two handlers," Hertz said.

"Here look at this," Hertz said as he held up a little metallic disk.

Immediately chuck flashed on the device showing pictures of Hertz and the various development of electronic listening devices that the NSA used for surveillance. The flash was accompanied with the beginnings of a monster headache.

"You designed the surveillance systems."

"Well not all of them Chuck. Just the original ones, however every new generation still uses my programming. You have to love cost cutting measures," Hertz chuckled.

"So you want the Intersect," Chuck shouted.

"No Chuck I don't want the Intersect. That is not why you are here. You are here because you are going to pay for the sins of Agent Frost. And for that Chuck I will say I am truly sorry," Hertz said with a slight look of sadness in his eyes.

"Agent Frost! Who the hell is agent Frost," Chuck demanded.

"Your father took the identity of Agent Frost out of the Intersect. Agent Frost took something from me and now I am going to take something from her," Hertz said.

"From her? Frost is a woman," Chuck said surprisingly.

"Some of the best assassins in history have been women Chuck. I am sure you would agree with that," as Hertz zoomed one of the surveillance feed monitors on a picture of Sarah.

"If you touch her I swear to God…"

"Oh please Chuck we can dispense with the theatrics. I have no intention of going after your girlfriend or your sister or anyone else. I'm not a monster," Hertz said as he dismissed Chucks demand.

"So the Intersect is important to Frost. That's why you are doing this," Chuck pleaded.

"Well it could be but I doubt the Intersect is of any real value to Frost. Chuck you however are of extreme value to Frost," Hertz smiled.

"I have no idea what you are talking about I don't know Frost," Chuck yelled frustrated.

"Chuck you have known Frost your whole life," Hertz said with a tinge on menace.


	8. Chapter 8

_Still don't own Chuck and make no $ from it_

Beckman was livid that something like this could happen. She had moved operations back up to the conference room and began to quickly assemble a plan of action. Casey and Sarah were down in the recovery room coordinating with the forensics team, while Beckman was trying to keep the investigation "in house". She had just finished emasculating a poor underling when she noticed her laptop blink on and a video began to play.

The grainy presentation lasted less then five minutes, but in that time her worst fears were confirmed. In order to complete this mission she needed the one person in the world who could succeed. She quickly dialed her phone and waited for a familiar voice to respond.

"Initiate identity protocol."

"Beckman secure. Burbank. Gordon Hertz. "

"Understood. Ancillary operational objectives (AOO)," came the reply.

"Two. Gordon Hertz (Alpha) Daniel Shaw (Beta). Asset specific information," Beckman replied.

"Understood. Time frame?"

"12 hours. All know information in regards to AOO sent to your database."

"Understood."

"Beckman out," she said as she hung up the phone.

Beckman closed her eyes and exhaled deeply as a single thought filtered through her mind, _this is about to get messy._

In downtown Denver Colorado, a tall middle-aged woman calmly hung up the phone and immediately accessed her secure database. She looked through pictures and information on Daniel Shaw, before selecting a recent picture and importing it into a search algorithm, as well as information on the man himself. The algorithm was designed for her by Orion and combined facial recognition as well as personal information to create a virtual profile of the subject.

The program would seamlessly access both domestic and foreign networks to gain all possible information. The program would then analyze the imported information, and based on probabilities that the program developed during the analysis, create a behavioral pattern of the subject. This behavior profile would then be analyzed to enable the subject to be located.

After a few minutes the program got a hit. An electronic signature from a Russian encrypted satellite phone that was requisitioned by Gordon Hertz over 10 years ago had been detected. Normally these phones are untraceable, but that particular model had larger capacitors inside which held a charge longer and thus generated an electric field, even when the phone was switched off. This allowed the phone to be tracked. The program then triangulated position and locked in the coordinates, which showed a location just north of Los Angles. The woman picked up her phone and dialed a secure number.

"Frost secure. Transport to Los Angles. 20 minute departure."

"Understood. You operational authorization is confirmed. Plane will be waiting."

"Frost out."

She hung up the phone and then picked up a small tablet like device, and headed for her plane.

Shaw had just pulled into the parking lot of the motel after delivering Chuck to Hertz. He had a few hours until he needed to be back and he wanted to gloat a bit after his successful mission. The motel was located in a very seedy part of town and would not attract too much attention, or so he thought. She was behind the door as he entered the room, silently waiting for him in the dark. Shaw turned around and violently fell to the floor as Frost hit him with 50000 volts from her Taser. She bound his hands and feet together and rolled him on his back to face her, while removing the phone that he still foolishly carried in his back pocket.

He looked at her with un-focusing eyes as he tried to process what was happening. _How had they found him so fast? I was careful….I need to get out of this_

"You..need,.." was as far as he got as he saw a boot enter his field of view, and then his world go black.

"Extraction. One heavy," Frost said into her phone.


	9. Chapter 9

Shaw had just pulled into the parking lot of the motel after delivering Chuck to Hertz. He had a few hours until he needed to be back and he wanted to gloat a bit after his successful mission. The motel was located in a very seedy part of town and would not attract too much attention, or so he thought. She was behind the door as he entered the room, silently waiting for him in the dark. Shaw turned around and violently fell to the floor as Frost hit him with 50000 volts from her Taser. She bound his hands and feet together and rolled him on his back to face her, while removing the phone that he still foolishly carried in his back pocket.

He looked at her with un-focusing eyes as he tried to process what was happening. _How had they found him so fast? I was careful….I need to get out of this_

"You..need,.." was as far as he got as he saw a boot enter his field of view, and then his world go black.

"Extraction. One heavy," Frost said into her phone.

Sarah was beside herself with overflowing emotions. Anger, rage, sadness and fear were all flowing through her at the same time. She had never really been in this situation before, it had never been this close to home for her. She had partners get captured before, but nobody like Chuck, like her Chuck. _What were they doing to him? Was he hurt?_ She knew that torture was part of the game, but it could never be for him. He was a sweet, innocent man and as she imagined the horror that was happening to him now tears flowed freely from her bloodshot eyes. The hours he had been gone had been the worst of her life.

She felt absolutely useless and felt she should have protected him better. He was missing because she failed, but she would never let that happen again. She resolved that she will do anything to get him back and she promised herself that God will have mercy on those that took him, but she will not.

"Walker briefing in 2 minutes," Casey said as he broke her out of her rage and they both made their way to the conference room to see a bleary eyed Beckman.

"Agents we have an update on Agent Bartowski's situation. A few hours ago we were sent a video of Agent Bartowski and the man holding him. The man's name is Gordon Hertz and he was one of the original programmers of the first generation Intersect," Beckman began.

"What we have been able to determine is that Hertz is not interested in using or selling the Intersect, so it appears Chucks cover is still intact," Beckman continued.

"Chuck's cover General! That's what your main concern is at this moment," Sarah said angrily.

"Agent Walker I can understand your emotions at this point in time, but now is not the time to be emotional. I need you thinking clearly or you are of no use to Chuck right now," Beckman scolded.

"Relax Walker. We will get him back," Casey said as he put a rather soft hand on her shoulder.

"Yes Ma'am. I apologize," Sarah said.

"You don't have to apologize for your emotions. You just need to control them," Beckman said with a slight understanding smile.

"Now as I was saying. We believe based on the video and the history that we have with Hertz that this abduction is unrelated to the Intersect," the general said.

"Can we see the video General," Casey asked.

Beckman looked pensive for a moment before she answered.

"The video has some graphic images. Sarah can you handle it," Beckman asked.

Sarah's heart dropped when she heard "graphic images" and she involuntarily shuddered thinking of what that could mean. She couldn't be weak now. She needed to be strong for him. He needed her to save him and so she steeled herself to become as detached as possible and told Beckman that she could handle it.

The video began and showed a very bloody Chuck strapped to a chair as Hertz began to speak. Sarah involuntarily moaned as she saw Chuck in the chair but quickly recovered before Hertz began.

"General Beckman I am here to inform you that I have taken Chuck Bartowski as my prisoner. I have no list of demands or intention of selling him to the highest bidder. My desire is that you show this video to Agent Frost to understand the pain that was inflicted upon me when Frost killed my family. There will be no ransom and no attempt at a rescue. In exactly 12 hours I will broadcast a live video to you of the end of Charles Bartowski's life. Charles is not to blame for this, but he must pay for the sins of his family."

The screen went blank and the room fell into a tense silence.

"I wanted to inform the both of you that we have apprehended Daniel Shaw and will be interrogating him now," Beckman said.

"Casey and I will do the interrogation," Sarah said as she jumped to her feet.

"Sarah sit down. You are too close to this," Beckman said.

"But Chuck needs us…"

"Sarah the general is right. You are too close and Shaw will be no use to us dead," Casey said as he restrained her.

"I will do it."

"No you won't major. Now the both of you sit down and listen to me. Agent Frost will do the interrogation."

The two agents looked at her with a high level of frustration, but slowly sat down.

"General who is Frost and what does this have to do with Chuck," Sarah demanded.

Beckman turned to look at her two agents and decided to give them some time to process what they had just seen. She also decided that they both deserved to hear the truth.

"What I am about to tell you is classified and was kept from you for reasons of national security. For all intents and purposes Frost is a ghost and is not acknowledged."

"Frost is disavowed?"

"No Major Casey, Frost is designated omega, which means that Frost is classified as never having existed."

The two agents remained silent. There were whispers of an omega designation around the intelligence community, but most agents thought it was just a myth. Those designated omega where used when a job absolutely could not fail. They were the best of the best and could never be caught or tied to the United States in anyway, in short they were ghosts

"You both know of Orion and his relationship to Chuck. Well Hertz was extracted from East Germany to help with the development of the original intersect. I was involved in the extraction, and Frost was Orion's handler," Beckman said.

"His handler Ma'am," Sarah interrupted.

"Just please listen Sarah," Beckman said as she smiled softly at Sarah.

"Hertz was playing both sides. He and his wife were actually sleepers for the Russians. Hertz was supposed to steal the Intersect, while his wife was tasked with killing Steven Bartowski and his family. Frost discovered this and arrested Hertz and his wife. His wife escaped and called in a kill team for Bartowski. Frost intercepted and killed the entire team, including his wife."

"My God," Casey muttered.

" Ma'am I don't understand. Surely its not Orion's fault that Frost killed his wife, why does Hertz blame him and not his handler," Sarah cried.

"He doesn't blame Orion," Beckman said.

"So what are the sins of his family," Sarah questioned.

"Sarah Agent Frost was not only Orion's handler, she was also his wife."

"Wait a minute Ma'am are you telling me that…"

"Yes Agent Casey. Agent Frost is Chucks mother."


	10. Chapter 10

Daniel Shaw sat alone in a room with a large mirror on the wall and waited for the interrogation to begin. He assumed that they were looking at him right now and he just imagined what was going through their collective minds. He was in self-preservation mode and he realized the only chip that he had to play was the location of Chuck Bartowski. Oh he knew that they would rough him up a bit, maybe even break a bone or two, but he certainly knew that protocol stipulated that they would not kill him.

Suddenly he was brought out of his thoughts by the sound of the door opening, and to his surprise a middle-aged woman walk into the room. She seemed rather tall, almost 6 feet with shoulder length dirty blonde hair with streaks of grey, and soft blue eyes. Shaw had to admit to himself that he did find her rather attractive as she sat down across from him at the table rather demurely he thought, and began her questioning.

"Mr. Shaw where is Agent Bartowski," she said.

The woman across from him was not what he was expecting. Sarah or Casey he was prepared for, but she was an unknown entity. Regardless, he thought, she was still an agent and would still follow protocol so he wouldn't change his tactics.

"I don't think I want to tell you," Shaw said as he smiled arrogantly.

The woman started across the table at him and calmly folder her hands and rested them on her chin.

"Do you know who I am Daniel," she asked.

"No I don't. But if you want information about Bartowski then I want a deal. I know how this game is played so don't waist your time. You can try to drug me or torture me but I will hold out long enough for Bartowski to die. So give me what I want and maybe I'll deal," he said with a smirk as he drummed his hands softly on the table.

If he expected his comments to elicit a response from the woman across from he his was sorely disappointed. She just looked at him with the same detached look, almost like she didn't even see him there. There was something very frightening about her gaze and, almost instantly, he could see her soft blue eyes transform into a lifeless cold blue. The look transfixed him so much that he never saw the knife.

"AAHHHHHH," he screamed, the pain erupting from him as the woman plunged the knife through his right hand pinning it to the table.

Suddenly the once clean table was smothered with blood. Shaw was unable to free his hand and the pain made it impossible for him to focus on anything else.

"Mr. Shaw where is Agent Bartowski," she said to him again.

"Fuck you. I will never tell you. You just killed him," He spat with tears streaming down his face.

"Mr. Shaw I will kill you if you don't tell me where Agent Bartowski is," she said.

"Fuck you. You got nothing….Every second you jerk me around here is another second Bartowski loses… My hand will heal," he said through clenched teeth.

"Fine then there is no reason to keep you alive," she said calmly as she took another knife and stabbed him in the shoulder.

"AH….AHH," he screamed out in pain.

The pain was unbearable and finally he was hit with a real fear that she would indeed kill him. She was not following protocol and when he saw her approach with another knife he broke. If he wasn't so terrified he might have been ashamed for having so little resistance.

"OK…Stop…I will tell you if you let me live," he screamed

"Where," she simply said as she stopped her advance on him.

"Powellton Street near 5th. The address 4165, it's an old fire station," he said while he slumped over.

Frost had already identified the location based on the electronic signature of the old satellite phone that he was using, but she needed confirmation.

"Thank you Mr. Shaw. I am sorry this will be ending badly for you," she said as she moved behind him and put the knife at the back of his head.

"Wait you said you would let me live. That was our deal," Shaw pleaded.

"That was never our deal Mr. Shaw," she said as she pressed the knife into his flesh and Shaw's world went dark.

Looking through the mirror into the room Casey and Sarah stared with a mixture of shock and horror.

Frost came out of the interrogation room and looked at Casey and Sarah. Her eyes momentarily focused on the bracelet that Sarah wore on her wrist before focusing back on Casey.

"Major assemble your team! Dispatch drones to this location and thermal map it. Agent Walker I want satellite coverage for the previous 24 hours on that location."

"Yes Ma'am," Casey said as he and Sarah ran to complete their orders.

"Walker," Frost called out to her.

"Yes Ma'am," Sarah said as she momentarily stopped.

"We'll talk later," Frost said as she eyed Sarah's bracelet once more before heading down the hallway

"Well Walker, how do you like your future mother in law," Casey smirked at Sarah who just stared back at him with a shocked expression on her face.

Chuck was in pain. He was standing vertically with hands in shackles and extended above his head on a hook, while his bare feet were placed in a tub of ice. Dressed only in the flimsy hospital gown he was shivering and sweating simultaneously. Dried blood caked down his face, and his feet were completely numb, pulling most of the remaining body heat out of him.

"Well Chuck I'm sorry to say our time together is almost over," Hertz said.

"Oh great. Remind me to fill out your comment card," Chuck mumbled.

"Ha! I do enjoy your sense of humor. I wonder where it comes from? Your parents were so serious," Hertz said.

"I don't know maybe the mailman," Chuck replied exhaustedly.

"I doubt that. Your mother was fanatically committed to your father."

Chuck began to giggle, and then he began to laugh uncontrollably. It was a sign of the stress just overwhelming him and breaking him down.

"What is so humorous," Hertz queried.

"You…you think my mother…hahaha….my mother left us," Chuck replied as his laughter had transitioned to tears.

"Chuck you will learn that every action has a reason," Hertz said.

100 meters from the front of the old firehouse 4 non-descript black panel vans were parked. Casey was finalizing final deployments and briefing Frost as Sarah studied the latest thermal imaging results.

"We have 2 snipers located here and here, along with a combat drone at 300 meters, giving us 360° coverage. 4 -3man fire teams will enter at these locations isolate the threat, locate and recover Chuck. From the thermal imaging we have 3 tangos on top floor 7 on the second and 9 on first."

"We have 3 medics on stand by and his blood type is…."

"O+" Frost and Sarah answered in unison.

"Casey Deploy. Walker you are with me," Frost said as checked her weapons.


	11. Chapter 11

They transported Chuck to a white room, which looked right out of a mental asylum, Chuck thought. The walls, ceiling and floor were all painted a brilliant white and the overhead halogen lamps added to the uncomfortable clinical feel. There was a clear wall sized window through which he could see another smaller room. There appeared to be no way to access the small room from his, as the only door was the one that he came in through, and that was behind him.

He was tired, cold and exhausted as they dragged him into the room, his feet frost bitten from soaking in the ice bath for so long. Could no longer support his weight. Hertz was waiting for him as they strapped him down into a chair and positioned 2 cameras in front of him.

"Well Chuck it appears that we have reached the zenith of our evening together," Hertz laughed menacingly.

Chuck remained silent. This body was wrecked and filled with pain. He simply didn't have the strength or desire to respond. He closed his eyes and took a deep breath, trying to chase away the feeling of dread, but it wasn't working.

"You are wondering where they are? Your rescuers?" Hertz said.

"I told you they wouldn't be coming. This entire building is a big faraday cage able to scramble any electronic signal," Hertz said.

"Any last requests? Besides let you go," Hertz laughed.

Chuck looked up at him but suddenly felt light-headedness. He closed his eyes and shook his head to clear his mind, but something was different. He opened his eyes and could see little waves generating from the lights and cameras. He shook his head again, but the waves were still there.

"Very well then Chuck. We begin the final act."

Casey had finished deploying his team around the building. The complex was composed of 2 structures, a larger building with lights blazing in the windows, and a smaller annex that looked deserted. The teams were surrounding the larger building, as the annex was deemed lower priority. The previous fly over by the drone had shown 8 heat signatures in the larger building, and none in the annex, giving the indication that it was abandoned.

"All teams sit rep," Casey said as he keyed his radio.

"Alpha team in position."

"Beta team in position."

"Charlie team in position."

"Delta team in position."

"Good. Bad Karma what is your status," Casey called to his snipers.

"Bad Karma one. I have movement on top 2 floors. 8 signatures. 3 on top floor, 5 on second."

"Bad Karma 2 can you confirm," Casey asked.

Bad Karma 2. I can confirm, but leader I see something strange."

"Report," Casey called.

"In the smaller annex building directly behind the target, thermal imaging is blocked. When I switch to starlight scope I can see an exterior generator running, but it's not giving off heat."

"Roger that Bad Karma 2. Bad Karma 1 can you confirm."

"Stand by scoping now," the sniper called as he adjusted his rifle.

"Leader Bad Karma 1. I can confirm," the sniper said.

"Roger that," Casey replied.

"All teams hold your current positions," Casey called.

 _I'm missing something…Hertz wouldn't make it this easy….He wouldn't pint a target like this_ …Frost thought to herself

"Frost we have a situation," Casey called as he keyed her on a secure loop and explained the findings.

"Chuck is in there," Frost replied.

"Frost we haven't confirmed this., there are no heat signatures. Are you sure?"

"Yes Hertz is using a faraday cage. Give me 2 fire teams and I'll hit that building."

"We will hit that building," Casey replied.

"Alpha and Beta team break off and return to the van. Charlie and Delta hold your positions."

"Roger that," came the response as the teams extracted and met back up with Frost, Casey and Sarah.

Casey quickly briefed them on the situation and then deployed them around the smaller building.

"Bad Karma 1. Report."

"Leader Bad Karma I. I have detected reflections on the starlight scope indicating movement. Stand by. I have 1 tango 2nd floor balcony."

"Threat level," Casey asked.

"Negligible."

"Engage," Casey said.

"Tango down," the sniper called as a soft thud signaled the down man.

"Status," Casey asked.

"He's not moving you are clear."

"Roger that. All teams sit rep."

All the teams responded that they were ready for the assault to begin.

"Recovery of Agent Bartowski is top priority. 5th freedom authorized on enemy combatants."

"All teams Go! Go! Go!"

Alpha team swept the top floor of the annex building, while Beta entered the ground floor. The sounds of discharging weapons were heard as the team got the jump on Hertz's men. The Charlie and Delta teams hit the main building simultaneously and we're having similar results.

Hertz's men were mostly Eastern European mercenaries, while proficient militarily, were not equipped to handle the firepower and coordination in CQC that the Americans demonstrated. CQC relies on training, teamwork and trust of team members, something that put the mercenaries at a disadvantage. The American squads executed their maneuvers like a precisely tuned orchestra, and quickly subdued and eliminated the threat.

"Leader Alpha 1. All hostiles down. No casualties."

"Roger that. Have you located the package?"

"Negative sir still looking."

Casey got similar reports from Beta, Charlie and Delta teams.

Once the initial report came in from Alpha team Frost and Sarah went inside. Sarah was running through the building trying desperately to find him, but every room she came to was empty.

"Casey he isn't here. Where is he," she yelled in a panic.

"We will find him Walker, " Casey replied as he caught up with her.

Frost was strangely detached as she examined each room, looking for some kind of clue to lead her to her son. She made her way into the last room and noticed a slight odor. She followed the odor and slowly approached the back wall.

 _Ozone...I smell ozone. There must be electrical equipment behind this wall_ she thought.

"Charlie and Delta. Have you located the package," Casey called anxiously.

"No joy on the top 3 floors sir. We are checking the basement now."

 _The basement. There was no basement shown on the schematics of this building…_ Casey thought.

"Walker we have a hidden basement somewhere," Casey said.

Sarah and Casey ran down to find Frost and alert her to the basement..

"There is a .."

Frost put her fingers up to her lips and motioned for them to be quiet.

"They are behind this wall," Frost whispered.

Frost carefully approached the wall and examined its texture. It didn't look like concrete or stucco.

 _It looks like cardboard_ …she thought as she touched it.

"It's a false wall. This is cardboard," she said as she pulled it down exposing a door.

"Major have your teams secure the buildings and the perimeter. Both of you come with with me," she said as she opened the door and walked through.

"Now agents," Frost demanded.

The darkness engulfed them as they entered the room with guns drawn. slowly their eyes adjusted revealing a small staircase. Frost took point and cautiously descended, followed by Sarah 3 steps behind and Casey on their 6. The passage was narrowing as they descended and Casey had to adjust his position to fully fit through.

After about 70 steps a small ray of light sliced through the darkness like a knife, illuminating a large steel door.

"Casey optics," Frost commanded as Casey came forward and slipped a small diameter, flexible tube under the door.

He plugged the other end into a small screen and waited, but only static appeared.

"No good. The signal is scrambled," he said.

"Let's breach the door," Sarah said.

"Hold on Walker, we don't know what's waiting for us inside," Casey said.

"Chuck is running out of time Casey," Sarah replied tersely.

Suddenly the lights went on in the passage disorientating the agents momentarily.

"Hello Agent Walker and Agent Casey," a voice came from a concealed speaker.

"Please allow me to introduce myself. I am Gordon Hertz and I have been Mr. Bartowskis host for the evening."

"Agent Frost thank you so very much for coming. You have been greatly missed," Hertz said menacingly.

"Where is my son," Frost replied.

"He is right through this door. Please all of you join us," Hertz chuckled as the door creaked open.

Sarah was terrified of what she might find as they entered. All she could think about was Chuck.

 _He is alive...he must be alive..please be alive Chuck_ she thought.

The sound of the door clicking locked behind them startled her back into reality.

They were in a small room with barely any light. There appeared to be a glass wall directly opposite them. Suddenly the lights flashed on behind the glass wall and Sarah's worst fears were realized.

"Chuck," she screamed as she saw him strapped to a chair, still dressed in the hospital gown with bloodstains on the gown and caked on his face.

Frost shivered involuntarily at the sight.

"Oh my god," Casey mumbled.

Sarah never imagined that one sight could truly devastate her. She was an agent and trained assassin. Cold, calculated and unfeeling, she could handle anything except the sight before her now. Chuck looked like he was dead. His feet were purple from the ice bath and his body looked broken. She knew she could handle whatever happened to her, but as the tears rolled down her face it was a testament to just how much she had changed. She knew beyond a shadow of a doubt that she couldn't live without him. She was filled with so many emotions and feelings as she looked at him, but the overwhelming one was despair.

 _I just need to get to him...I cant get to him_..she thought as she the frustration began as well.

"Chuck can you here me? What have you done to him," Sarah screamed as she banged on the glass.

"Sarah," Chuck mumbled as he heard her voice.

He opened his eyes and saw 3 grainy shapes beyond the window. He could not make out the other two, but he could definitely see Sarah, she was crystal clear.

"Well our boy is awake," Hertz said as he pulled out a syringe from his pocket.

"Hello Frost. I have been waiting for this for 30 years! Do you know what this is," Hertz asked while holding up the syringe for all to see.

Frost shook her head.

"This is the same poison you dipped your bullets in when you killed my wife! She would have survived the gunshots, but the poison. It destroyed her from the inside out, burning her veins and torturing her mind! I love the irony that now you have to see it first hand."

"Let him go Gordon. It's me you want. Take me and let him go," Frost said as the sight of her son in this position almost caused her to break.

"I have been dreaming about this for so long. You can't possibly imagine how much I have looked forward to this."

"Let him go and take me. He has nothing to do with this" Frost demanded.

"He has everything to do with this," Hertz exploded.

"You took away the one thing in my life that was most important! You want to know what I want? I want to see you suffer! I want to see your pain when I take away your son! I want you to watch him die!"

"To hell with that," Casey said as he fired 3 rounds into the window.

3 small dents appeared in front of Hertz face, but didn't penetrate the window.

"High density acrylic resin. It's able to withstand depleted uranium anti tank rounds. Don't you just love technology," Hertz quipped.

"Well now let's not drag this out any further. Sorry Chuck."

"No!" Sarah screamed as Hertz inserted the needle into Chucks arm and pushed the plunger.


	12. Chapter 12

Chuck felt the burn as soon as Hertz pushed the plunger. It felt like something was trying to rip apart his skin. He looked at the syringe as Hertz pulled it out of his arm and felt the flash come and his eyes closed.

"Chuck," Sarah screamed when she saw him close his eyes.

"You son of a bitch," Casey yelled as he pounded on the window.

"No Charles," Frost cried as a tear streaked down her cheek.

Although Chuck couldn't open his eyes, he could hear everything they were saying and the information from the intersect poured into his brain.

 _RX232 is a poison derived from king Cobra venom. Can be neutralized with 3n14 antibody serum developed by CIA. Kill time 1-3 hours depending on dosage. Compromised immune system accelerates the process. Lower heart rate and respiration to prolong life until 3n14 administered._

A picture of a cardiovascular system appeared in his mind and suddenly his heart began to slow down and his respiration got shallower. He began to shake as the intersect took control of his systems and involuntary muscles to maximize his body's ability delay the poison from killing him. His head slumped down as his body, governed by the intersect, went into self-defense mode and shut down all non-essential systems. The heart monitor that Hertz had him hooked to flat lined signaling the death of Chuck Bartowski.

"Well I would have expected you to last longer," Hertz said.

""Oh God No! Chuck," Sarah screamed as her hands turned bloody from banging on the window.

Casey was kicking the window as hard as he could to break it after having exhausted his clip into it. It was no use however, the window was impenetrable.

Frost was frozen in place, silently crying as she saw her son die.

"Nothing to say Frost? Nothing to say after I kills your son," Hertz sneered.

Although he looked dead, he was very much alive with his heart rate and breathing lowered and controlled to an undetectable rate. The electrical impulses his brain was sending to his heart was disrupting the reading from the heart monitor.

 _Her Son...Frost ...I need to see_ Chuck thought.

 _I need my eyes_...he thought an instantaneously his eyes opened.

He focused his vision on the Window and could now clearly make out all the figures. Sarah and Casey we're naming on the window and another woman was in the corner crying.

 _She looks .so sad...who..is that...Frost..Mom?_

Frost couldn't respond to Hertz, she was trying to numb herself to the pain but she couldn't. She was shutting down.

"Very well. Enjoy your death," Hertz said as he hit a button.

The loud sounds of air being evacuated from their room startled Casey, but Sarah and Frost were still numb from Chuck.

"Walker he is going to suffocate us!"

"We're sealed in. Shit it won't budge," Casey said as he desperately tried to open the door to the room.

"Walker help me! Move your ass!"

Sarah didn't seem to care that her life was about to end. Having seen Chucks demise the prospect of death was much enter then the alternative of living without him. Her eyes never left him as the air began to get dangerously low.

"You will be unconscious in 3 minutes and dead in 5," Hertz said with satisfaction.

 _I need to help them...I need to help them...how can I_ ..chuck thought.

Immediately his mind began to flash.

 _I need to break the glass... I need to break the glass_ he thought, and as he had this realization the little waves that he could see around the electrical devices began to grow larger.

He could feel it building inside of him. His heart rate began to increase, pumping blood back to the systems that needed to be used. Respiration increased, and if Hertz was not so concerned with gloating over Frost, he would have seen Chucks heart monitor come back to life. Very slowly he had feeling come back to his arms and legs, and he slowly opened his eyes.

 _Movement!. He moved_...Sarah thought as she saw him move.

She was happy, despite the current situation she gave Chuck the smile that was only for him. It was a smile a man sees when his bride is walking towards him on their wedding day, or when she holds their child for the first time. It was the smile reserved especially for her soul mate.

There was not much air left , but as she sensed her death approach, she wanted her last act on this earth to give him something that could convey all that she felt for him. She could not touch him or talk to him, but when he returned her smile she knew he understood.

Sarah took once last breath, then slowly began to slide down, her eyes never leaving his, as she slipped into unconsciousness.

 _Sarah NO!_

 _They are going to die..they are going to die because of me...they came to save me and he is going to kill them._

"I've been waiting for this moment Frost," Hertz sneered.

Chuck could feel something begin to happen to him, a rage began to build up from deep inside. She was in danger he needed to get her out before the air was gone.

 _No!...No! No!_

He looked closer at the window and pictured in his mind the resin, he focused harder and instantly the particles began to vibrate.

 _Faster_ he thought..and soon the particles were moving like waves up and down the window.

Hertz noticed it first. There was a vibration on the window, which seemed to be reacting as if someone was hitting it with a Sledgehammer, but no one was.

Frost, Casey and Sarah were on the floor drifting into unconsciousness when the window began to crack.

Hertz looked at the window and it seemed to be pulsating., and he heard the sounds of breaking glass as the halogen lamps began to explode.

He looked back and was shocked to see that Chuck was alive. He saw the intense stare at the window and looked at a nearby monitor to see Chuck's body temperature had risen to 105. Hertz shook with fear as Chuck's body seemed to be vibrating and his eyes shown like diamonds.

Hertz raised his gun toward Chuck and pulled the trigger.

Instantly a picture of a bullet materialized in Chucks mind. Millions of metallic particles that comprised the bullet began to heat up to and the structural integrity failed. Within one meter of being discharged, the bullet had deteriorate to a liquid metal mas.

Hertz stared in disbelief as the liquid mas harmlessly splashed into Chuck's chest. Immediately he felt his gun burn his hand as it was now glowing red, and dropped it. He ran for the door at the south end of the room and pulled it open, running out just as the window began rattle again.

The image of the window returned to the forefront of Chucks mind, and as he felt the urgent need to free Sarah, the waves of particles began to converge and physically alter the structure of the window. The window was violently pulsating now and with a hideous shriek, the window exploded clearing the room of gas and sending shards of resin onto Chuck.

"Sarah! Sarah can you hear me," Chuck screamed.

20 seconds later Alpha team breached the back door and poured into the room.

"Help them first please! They are in that room please hurry," he cried.

"Alpha 1. 3 down need medics and respiration stat!"

"Agent Bartowski how are you," a medic asked as he began cutting his restraints.

"I'm ok. How are they? How is Sarah?"

"They are going to be fine. I need you to calm down," the medic said as he tried to take his vitals, but was having trouble.

"I'm ok. A little tie….tt…tired," he slurred as he began to slide down the chair

"Agent Bartowski stay with me! We need evac here!"

When he broke the window he increased his heart rate, which pushed the poison through his veins faster. The poison was now taking hold and draining away his strength.

"Chuck! Oh my God what's wrong? What's wrong with him," Sarah cried as she cradled him in her arms.

"Ssshhrraa…u…ook," he slurred.

"Yes! You saved me! You saved us all! Don't you leave me Chuck," Sarah cried.

"tss ooh…ook. I lovvv uh..u," he said as he closed his eyes.

"Oh no Chuck! Casey I think he's dead," Sarah cried as she hugged him tightly.

"Buuuullllll..Shit," Casey yelled as he picked up Chuck and ran towards the evac chopper.

"Move you asses ladies," Casey called back to Sarah and Frost while running.

"Not like this you bastard! Not yet," Casey whispered to Chuck.


	13. Chapter 13

_A/N: Thanks everyone for the reviews and kind words. Story is progressing pretty well, but its not over yet so pleased stay tuned. Once again I don't own Chuck and don't make any $ from it._

The waiting room in the hospital looked like a Rockwell painting on steroids. Beckman was frantically talking on her phone, while Casey was talking to Alpha team leader. Frost and Sarah were sitting off to the side in a empty bank of chairs, with one empty chair between them. Neither one of them were speaking, they were just trying not to think the worst. Alpha team was positioned outside Chuck's trauma room, Beta secured the waiting room and Charlie and Delta were still at Hertz's warehouse securing the site and searching for Hertz.

Casey had managed to administer 1 vial of 3n14 on the chopper, which ultimately may have saved his life. He flat lined once in the chopper, but hospital staff had managed to stabilize him. The issue however was still in doubt as Chuck had slipped into a coma due to the damage done by the poison. After he was stabilized, his initial brain scan revealed that there was damage to his brain that resulted in bleeding. This was most likely what was causing the coma.

Dr. Reber called them into a conference room for an update. and as soon as they were all in, Beckman took the floor.

"Dr. Reber, if you would," she pressed.

"General we believe that vial of 3n14 that Agent Casey administered on the chopper, coupled with the 3 vials administered here has successfully neutralized the poison."

Thank God..Sarah thought.

"However," Reber began. as he activated a switch illuminating Chuck's body scans on a presentation screen

Oh No…Sarah thought.

"The effects of the poison were extensive on Agent Bartowski's system. Particularly on his cardio system and his brain, if you notice these dark patches on the brain and on the heart, we believe that this is scar tissue. The tissue on the brain is most problematic, as brain cells do not regenerate, its possible this could lead to significant brain damage. We are doing all we can for him right now, the next few hours will be critical."

"Dr. Reber when will Chuck wake up," Beckman asked.

"I'm sorry General, but we don't know. It could be days or he may never wake up. I'm so sorry Sarah," Reber said as he looked softly at Sarah.

"Oh dear God," Sarah cried as she buried her face in her hands.

A soft hand was on her shoulder squeezing gently in a soothing motion.

"Hang in there Sarah. Chuck needs you to be strong for him. Everything will be ok," a voice said.

Sarah grabbed the hand and was surprised to look into the blue eyes of Frost. The two women finally embraced, the emotion of the last few days had finally come to a head. They both wept openly and comforted each other, as both women couldn't hold the emotion in anymore. In different ways they both loved this man desperately, and as the tears fell an unmistakable and lasting bond was formed. This was the moment that the two most important women in Chuck's life accepted each other, in that instant shared the depth of love they had for Chuck. When they finally released each other they looked around an empty conference room.

Beckman was back in the waiting room and walking towards the coffee machine when Casey intercepted her.

"Pardon me Ma'am I thought you should know ASAP. Delta team captured Hertz. He was located hiding in a drainage ditch."

"Major Casey, have that sack of shit taken to Castle!"

"Yes Ma'am."

"Would you like to join me," she asked, once Casey had arranged the transfer.

"With every fiber of my being," he said while trying to contain a small smile.

"Let's go Major!"

"Come with me

Chuck felt like he was floating. His arms and legs didn't have any weight to them, it was as if he was in zero gravity. He opened his eyes to a black void, there was infinite space all around him, but he could not see any light. He was totally alone.

"Hello," he called into the darkness.

Suddenly millions of images exploded out of the void. Images of Sarah, Casey, Ellie, his mother and father. Chuck called to each one of them but they didn't respond and as quick as they came they left.

"No wait please! Someone help me," he cried.

A small white dot appeared through the darkness and began to grow. Slowly it swirled until it began to form an image.

"Oh my God," Chuck exclaimed.

"Hello Charles," the image replied.

"Dad?"

"Welcome to the intersect."


	14. Chapter 14

_A/N: Thanks everyone for the kind reviews and PM. The story is chugging along like the little engine that could, but not too much more… I'm thinking maybe 3 chapters left… I don't own Chuck nor make any $ from it._

"I'm in the intersect? How? What's happening to me? Wait does that mean that you are not real," Chuck asked.

"I am real Chuck, but I am program," his father replied.

"But why do you look like my father?"

"I was developed by Steven Bartowski and as you had personal experiences with Steven Bartowski he selected his image to be associated with me."

"I don't understand. Are you the intersect program," Chuck said.

"I am part of the intersect, but I perform a very specific function. I am your security assist interface, or SAI."

"I didn't read about this in the program booklet."

"You will not find me in the booklet, Steven Bartowski designed me specifically for you. I am a remnant from the original purpose of the program."

"The original purpose? What was the original purpose? What is happening to me?"

"The intersect was originally designed as possible resolution for paralysis. Neural commands are transmitted from the brain through the spinal cord, when a spinal cord is injured these neural transitions can't get to the target destination. The intersect was designed to overcome this by adapting remaining pathways to be able to handle neural transmissions."

"When the government took over the program, this original program was left in and adapted specifically to keep you safe. My current function is to heal your body."

"To keep me safe? Heal my body? How? Why" Chuck asked.

"Yes. This program will immediately take control of the Intersect when a deadly threat is detected, either external or internal. Based on visual and auditory stimuli, that are continually monitored, a threat assessment is calculated. If the threat is external neural transmissions will be focused on elimination of the threat to you physical person. This could entail moving your body or engaging the combatant. If the threat is internal neural transmissions will be focused on preserving your life until the threat is eradicated."

"The program is specifically tailored to you based on information that was created by your first download, Dated May 4th 1987."

"Wait did you say 1987?"

"Correct. You first downloaded the intersect May 4th 1987. Information obtained as a result of that download was the genesis for my purpose, Steven Bartowski specifically created me to keep you safe."

"I don't understand, to keep me safe from what," Chuck said frustrated.

"In order to provide you the answer to that question I need to show you a video file that was coded in specifically for this purpose. This message is from Steven Bartowski."

Immediately a picture of Steven Bartowski appeared to Chuck, it was if he was watching him on a laptop.

"Hello son, if you are watching this video then you have most likely gone through a traumatic event. I'm very sorry for that Chuck. I never wanted you to get stuck with the Intersect, and I fought for years to keep it away from you, but I lost the fight. I'm very sorry son. I know that you probably have many questions, and I hope that this video and your SAI will be able to answer many of them.

" I will start the story at the beginning and hope that you will understand that your mother and I didn't want to leave you and Ellie, but we had to keep you safe

Chuck you are special. Your brain is very unique, it can handle and process information more efficiently then most people in the world. You will not remember this but you downloaded the Intersect before, when you were very little."

"The download was a mistake, but unfortunately when you downloaded it your brain scan was immediately uploaded to a NSA secure data base. It was only a mater of time until they found you, and your mother and I tried like hell to keep you hidden. I never wanted the Intersect to become what it turned into; I originally designed a system to help people who had a stroke. When my father had a stroke I watched it keep him prisoner in his own mind. I wanted to free him from his prison, I wanted to help people, but once the government took over the project everything changed."

"I wanted to make sure that you would never be host, but once I realized that was impossible, I was determined to make you as safe as possible. So I designed SAI specifically for you, SAI is my gift to you."

"I don't understand? How" Chuck asked.

"SAI determined that the 2.0 version contained a malicious code. The initial flash caused a rupture in your brain, by diverting neural pathways and streamlining functionality, damaged tissue could be repaired, and brain cells were able to be regenerated. This modification required an altering of the topography of your brain, which resulted in additional neural capabilities."

"What kind of neural capabilities? Can you tell me about them"

"I will tell you about everything."

"Hello Gordon," Beckman said as she entered the interrogation room.

Hertz was cuffed to a chair and filthy from hiding in a drainage ditch, he looked up and smiled weakly at his former friend.

"Diane you look lovely. That uniform is very becoming on you."

"Gordon I will be blunt. You have become a real pain in my ass. You are responsible for the death on an entire surgical team and of course the abduction, torture and attempted murder of Agent Bartowski.

Hertz smiled smugly at Beckman.

"I did what I had to do to get justice for my wife."

"You and your wife were plants by the Russians. You tried to steal our technology and murder the designer, as far as I'm concerned she got what she deserved."

Hertz's smug expression remained on his face, with hardly an acknowledgement of Beckman's mention of his wife.

"You saw what he did in there Diane. He is better then any of those old simulations we did. Steven never told me where he got the model for system, but I can see now it was his son all along."

Beckman stared hard at Hertz for a few seconds.

"I would suggest that you concern yourself more with your future, then with anybody else's," she replied.

"You won't be able to control him Diane. He is too powerful, you should have let me kill him," Hertz laughed.

"That's enough!" Beckman said as she slammed her fist on the table.

"You know I am right. Once the higher ups realize what kind of monster they created they will order his termination immediately. He will never be allowed to survive, so in the end I win either way. Frost will still suffer the loss of her son and ultimately you will be responsible because you created him," Hertz laughed menacingly.

Beckman looked across the table at him and saw a sad representation of a man. He was devoid of any compassion or humility.

"Gordon you are correct, it is my responsibility. Just like it was my responsibility to my friends to watch over their son when they had to go into hiding. I made a promise to Chuck's mother to never let him become her greatest fear."

"Well obviously you failed," Hertz chuckled.

"No Gordon. He still has his humility and compassion. I have reviewed the tapes from the warehouse and he could have killed you if he wanted, but he didn't. His only concern was saving the lives of his team and his mother. That is what makes him different and that is why he is so special."

"You think just because he has a heart he can't be corrupted? Open your eyes Diane everyone can be corrupted. He will lose himself just like all the rest of us," Hertz said.

"No Gordon. That is why I am here. He is not like the rest of us. He would never do this," Beckman said as she raised her P88 and squeezed of a round directly into Hertz's brain.

Immediately Casey walked into the room.

"I will need a clean up crew Major."

"Yes Ma'am."

"I will also need the surveillance from the interrogation room," she said.

"Yes Ma'am."

"Oh Major Casey we have a location of former director Lomax. He is believed to be hiding near this particular monastery in France. Why don't you go light a candle for our favorite monk," Beckman said as she handed him a folder.

"Yes Ma'am," Casey said with a slight smile.

"Carry on Major!"


	15. Chapter 15

_A/N: I don't own or make any money from Chuck_

On the way back to the hospital Beckman got an urgent call from Reber that there was a major change in Chucks condition. Fearing the worst, she recalled Casey to the hospital and arrived just after 1am. Once everyone was in the conference room, Reber started the meeting immediately.

"Ok we have some interesting developments that are going on. I want to draw your attention to these two brain scans," Reber said as the appeared in the presentation screen.

"The first is one taken when Agent Bartowski was first admitted. Notice these dark sections here indicative of neural bleeding am tissue damage."

"Now look at this scan taken this morning, roughly 40 hours since Bartowski has been admitted."

The group looked at the scan of what appeared to be a totally healthy brain; there was no indication of damage at all. Everything looked nice and green, with no dark spots or indication of damage.

"Doctor I don't understand, what's going on," Beckman asked.

"From every indication that we get general, it appears that agent Bartowskis brain is healing, but not just his brain. There is increased blood flow in his feet, which appears to be fighting off gangrene. We have never seen anything like it."

"Doctor does this mean that Chuck is going to be ok," Sarah asked meekly with her heart in her throat.

"Well I can't say definitively yet Sarah. We still have to gauge him when he wakes up, but he is definitely improving," Reber said as he offered her a smile.

"I'm sorry I can't be more definitive, but think of it this way. A few days ago we didn't know if he would wake up, and now it looks like he will be waking soon. We are going to move him out of ICU and into recovery."

There was an audible gasp as a collective breath was released. Tired and teary eyes were in abundance as Chuck's condition had markedly improved.

"Well done Dr. Reber, it's simply amazing," Beckman said as de came up to shake his hand.

"Thank you General, but could I have a word with you in private," Reber said.

"Yes. If you would please excuse us," she said as the rest of the people filed out of the conference room.

"What is it Doctor," Beckman asked.

"General we have not changed anything since our initial stabilization of Agent Bartowski."

"Your point being?"

"General Agent Bartowski is healing himself!"

"What?"

"Look at the read out from his neural kinetics. His brain is incredibly active and processing an enormous amount of information. We can trace increased areas of body temp specifically to regions of injuries."

"Wouldn't that be indicative of an infection," Beckman asked.

"Not like this ma'am," Reber replied.

"The healing process has been accelerated so much that pathways used to remove damaged tissue and transport it to waste, have risen in temperature so much that we can track them with heat signatures. I have never seen anything like this."

Beckman looked at the man like he had just grown a second head. Everything over these last few days had been nothing short of amazing.

"Dr. Reber. I have a feeling there is a lot we haven't seen yet."

Beckman was back in the conference room, which she had transitioned to her temporary command center when she heard the knock on her door.

"Agent Frost to see you Ma'am," her aide said as he opened the door.

"Thank you sergeant," Beckman said as Frost entered and the sergeant closed the door.

"How are you holding up Mary," Beckman asked.

"I'm ok," Mary replied.

"You don't look ok."

"Thanks Diane."

Beckman took two glasses out and filled each with an amber liquid, as Mary sat down across from her.

"Wine is for pussies," Beckman said as they touched glasses and each took a sip.

"So what's on your mind?"

"I don't know Diane. I am just tired I guess. I thought it was over, that maybe everyone was done with this. Now everything with Hertz just brought it back again."

"Chuck is never going to be free is he Diane? It's all my fault," Mary said as a tear rolled down her cheek.

"I ruined my husbands life and now I am ruining my sons life."

"Why because you recruited Steven? For Gods sake Mary they would have killed him if it wasn't for you, they wanted his invention and as soon as they had it he was going to be terminated. The agency was not going to stop and you know it."

"I should never have accepted the assignment," Mary said.

"Really? Never have accepted the assignment? I have never seen two people more in love then you and Steven. You two were amazing together. Which part do you wish you never did? Met him, loved him, married him, or had his children?"

"You and Steven both knew that Chuck getting the Intersect was only a matter of time. Once they located his uploaded brain scans the government was going to find him. You did the best you could to protect him, but you can't protect him forever."

"I know that Diane."

"I know you did, and I know that because you requested Walker. I will admit I didn't realize it at first, but Sarah was a good choice. I thought it was just because she was so highly rated, but after about ten minutes I realized why you really wanted her for Chucks protection" Beckman said.

"Yes. Well Graham owed me for years of covering his ass," Mary replied as she sipped her drink.

"It's a shame what happened to him," Beckman mused.

"Yes well things happen to people who give termination orders," Mary said coldly.

"By the way thanks for telling me your plan. I had no idea how I was going to keep everything from going to shit. I even had to order Casey to Chuck's apartment and was about to call him off when I got word about Graham. You were just supposed to destroy the Beta, I didn't know about Graham."

"Old wounds Diane. He was dirty. How many of us did he manipulate into his kill squads. He deserved what he got."

"What about Casey? Can we trust him?"

"Casey resigned the night I gave him the order. It was only after I suggested another team do the cleaning that he relented. He wanted your son not to suffer, and afterwards I had to listen to him tell me in no uncertain terms that if that order was ever given again he would get Chuck to safety first. Then he would tell Walker."

"Really?"

"Yes."

"Well she seems to be very fond of my son."

"That's the understatement of the year."

"What do you think Diane? Do you think it's real with her? You know her history," Mary asked.

"Yes, I have seen it in her since the first day. She loves him very much, and I can tell that it scares the hell out of her. I can tell you right now that I can't trust Sarah to do what I order her to do with Chuck, but I can trust her with his life."

"If that order went to Sarah instead of Casey I would never see Chuck again; and then I would have to worry about her coming after me."

"She seems a bit of a risk, why do you tolerate her?"

"Because she is the best person to do the job of protecting your son and keeping him calm. As you are well aware your son has a tendency to get a little unhinged, yet another trait he gets from his father," Beckman smiled.

"That's true," Mary said while chuckling.

"Anyway Sarah is the most important part of Chuck, simply put he doesn't work without her and she doesn't work without him."

"That sounds familiar," Mary said while showing a slight smile.

"I'm sure it does Mary, but again you already knew that. Listen it's about time you have a talk with Sarah. You need to get on the same page about Chuck. Tell her the truth. You know her better then anybody, and you have been where she is right now. Help her to do it the right way. Help her to have the life that both she and he deserve."

"I could always count on you to tell me what I needed to hear, thank you Diane. When did you get so smart?"

"Are you forgetting you copied off me for 4 years at the academy!"

"Your a good friend," Mary said while embracing her.

"I'm a great friend. What's this good shit," Diane replied while returning the embrace.

"Now go talk your future daughter in law," Beckman said while they both laughed.

Mary reached the door and turned back to Diane.

"Who would have guessed that possibly the most dangerous assassin in world would fall in love with a tech guy," She said.

"It's not that strange. After all he is his fathers son," Beckman replied.

"That he is," Mary replied as she went out the door.

Sarah awoke to the familiar sounds and smells of the hospital room that she had been sharing with Chuck for the last 3 days. The beep of the heart monitor, although annoying, also gave her comfort showing a strong heart beat. She had kept a vigil for him and refused to leave the room till he woke up.

The medical staff had brought her meals and supplied her with scrubs so she wouldn't need to leave. She had just finished showering and changing into new scrubs when she made her way out of the bathroom to find Frost standing over the bed.

Mary was looking intently at Chuck and Sarah could see the corner of her eyes mist, as she slowly ran a finger through his hair.

Sarah stood in silence for a few minutes and was about to say something when Mary spoke.

"You know when he was a baby I put refused to get his hair cut for such a long time people began to think he was a girl. His father and sister both tried to get me to cut it but I wouldn't for the longest time. I love the curls," Mary said.

"I know. So do I," Sarah replied.

Mary turned and looked at Sarah, her eyes drawn to the bracelet around her wrist.

"You know I never wanted to leave them. Things escalated so quickly..,"

"You don't have to explain anything to me. I understand," Sarah replied.

"Sarah do you love my son?"

"Yes I do," she replied.

"Then you need to listen to what I am about to tell you."

Sarah silently nodded.

"I was in the agency for about 4 years when I got the assignment that was Steven Bartowski. His father had a stroke and he was working on a way to help stroke victims regain motor functions through visualization," she said as she slightly smiled.

"He wrote an article in this little tech journal amount a program he had written that function like a human brain. He liked to say it worked in patterns, the program searched data and correlated it with specific images that were uploaded. The data would then be transmitted as neural impulses to parts of the body helping them regain their mobility."

"That sounds amazing," Sarah replied.

"You have no idea the firestorm this created in the defense department. Everybody wanted to get this thinking computer. I was told to assess him, see if he was a threat or was working with a foreign agency, and eliminate him if he was," she continued.

"God he was so clueless! He had no idea what he had created, of how it could be used. All he ever thought about was how it could help people. He was so helpless like a little child," she said as a single tear ran down her cheek.

"You fell in love with him," Sarah said more of a statement then a question.

"Yes I did. I didn't expect it. I was so broken when I meet him. Burned out from all of this shit. He never saw me as I saw myself, from day one he saw me as the person that I really wanted to be. No lies, no covers, just me. Just Mary."

"Mrs. Bartowski.."

"Mary. Call me Mary please Sarah."

"Ok. Mary how did Hertz get involved with the Intersect?"

"They wanted to extract Hertz. Steven had met him back in grad school. Hertz had contacted him and tried to tell him that he could help his research. He began talking about his wife, and of course Steven was such an easy mark he fell for it."

"I thought you were his handler. Couldn't you have stopped him," Sarah asked.

"I took a reassignment a few months before Hertz made contact," Mary sighed.

"Why," Sarah asked timidly.

"Because I was in love with him. I could not bring myself to burn him if the order came. I was convinced that if I was away from him then he was safer. It all sounds so stupid now, had I been there Hertz never would have been an issue."

"General Beckman told me that you intercepted the hit squad, so I thought..."

"Diane was working Hertz and knew something was off. She contacted me. I couldn't let anything happen to him Sarah," Mary replied.

"I understand," Sarah said solemnly.

"After the incident I was designated omega and offered Europe for long term mission or stay on with Steven. I still thought I should go, but Diane was able to get me one day to say goodbye."

"You were going to leave," Sarah asked incredulously.

"I had to Sarah! I was back to being that person! That broken burned out killer. Surely someone like me didn't deserve happiness. So I went to see him to say goodbye."

"But...but...," Mary paused as she began to get overcome with emotion.

"But he loved me. I told him what I did and he still loved me," she said the tears flowing freely now.

Sarah was crying as well clutching her chest as Mary continued.

"I never imagined that I would ever be worthy of someone like him. I was so happy and for the first time in my life I felt like I was normal."

The room grew silent as Mary tried to compose herself, the only sound coming from the heart monitor and the sniffling of the two women.

"Every country on the face of the earth wanted the intersect, an if they couldn't get it they wanted Steven. If they couldn't get him they wanted his children. Steven and I knew we couldn't take Ellie and Chuck on the run and keep them safe. So we went into hiding to draw the focus away from the kids."

"We knew eventually that the Intersect would find Chuck."

"Why," asked Sarah.

"Sarah I need to tell you the entire story. Chuck is special, his brain is very special. When Steven was working on the prototype and testing his beta versions, he could never find a way to safely transfer the data. Steven ran computer simulations that showed it to an inordinate amount of neural kinetic capacity to be able to safely operate the Intersect."

"Steven was against human testing but Graham went ahead without our knowledge. Every subject that he tried it with had a cerebral hemorrhage."

"That son of a bitch," Sarah said.

"Steven was devastated. He kept working on trying to make it safer, but he couldn't. Then one day he had a breakthrough."

"What happened."

"Chuck accidentally downloaded it."

"What? Oh my God was he ok? Did anything happen," Sarah asked with concern.

"He was fine. He was 9 years old and didn't affect him at all."

"That's incredible," Sarah said.

"It really was. It also made him a target," Mary replied.

"I don't understand," Sarah said.

Mary went on to explain how Chucks brain now became the prototype for the working intersect, and how every entity with an interest in the Intersect now became focused on Chuck Bartowski.

"The key Sarah was the brain, not the software. Once they figured that out it became clear that the only way to keep Chuck safe was to give him the Intersect," Mary said.

"What? You deliberately gave him the Intersect? How could you put him in such danger," Sarah said protectively.

"We had no choice! Without the Intersect Chuck still had the brain that they needed! We couldn't stop them from getting him, but we wanted to make sure if he was going to get it that he would be as safe as we could make him. Steven tailored the intersect with safety measures and special features for him."

"What about his physical protection." Sarah demanded.

"What would have happened if Graham never assigned me here? What if he was just stuck with Casey? He would be in a bunker by now," Sarah said with anger.

"Graham didn't assign you Sarah. I did."

"What?"

"I have been watching you Sarah for a very long time. When I was looking for someone to protect Chuck you were always my choice."

"Why," Sarah asked still shocked by the revelation.

"Because looking at you I see myself 30 years ago, it's like looking into a mirror. I know you very well, I was you. I know how you were recruited, the terrible things that you had to do, and how broken you were. "

"Are you saying this was all some kind of a set up," Sarah said angrily.

"No Sarah. I knew the kind of person you were and I knew exactly what you needed. I also knew you are exactly what my son needs. I have seen the mission videos, the reports, I know you love him."

"I know you think that you don't know how to handle a relationship, and I know that you are terrified that you will screw it up. I have been down this road Sarah," Mary said.

"Why are you telling me this," Sarah asked through tears.

"I want to help you Sarah."

" But why?"

"Because my son loves you with all his heart and makes you happy," Mary said as she gently fingered the little figurines on Sarah's charm bracelet.

"And many years ago, his father did the same for me," Mary said as she exposed her necklace showing the same figurines as on Sarah's bracelet.


	16. Chapter 16

_I don't own Chuck, nor make any $ from it_

Casey made his way into Chucks recovery room carrying 3 cups of coffee, to find his partner curled up asleep under Chucks arm.

"Good morning Major," Mary said from behind the door startling him.

"Damn it! Oh Mrs. Bartowski, I'm

Sorry I didn't see you there," Casey said as some coffee spilled on his hands.

"Not your fault Major, I'm very good at not being seen. Is one of those for me?"

"Oh yes. I brought one for Sarah as well, but obviously she is indisposed at the moment," he said as he put down her coffee.

"Major would you mind if we had a brief chat," Mary asked.

"Of course not and please call me John," he said as he sat down.

"Only if you call me Mary," she said as she sat down and sipped her coffee.

"Well from everything that I am hearing it sounds like Bartow..I'm sorry Chuck is getting better," Casey said as he sipped his coffee.

"Yes it sounds like it. Of course we are still waiting for him to wake up," Mary said.

"Yes of course. I'm sure he will very soon," Casey said.

"Thank you John," Mary said.

Casey was uneasy in an environment like this. He was uncomfortable with personal conversation to begin with, but combine with all the ups and downs of the last few days and he was emotionally drained.

"John may I ask you a personal question," Mary asked.

"Of course," he said.

"Why didn't you kill my son?"

A burst of coffee flew through the air, followed by the

Sound of coughing as Casey processed the question.

"Excuse me ma'am," he replied.

"I know about the termination order from Graham. I also know about your protests and your response to Beckman, but then I looked at the surveillance tape."

"Mary I can explain," he began.

"You had him dead set. You were in the apartment with him for 3 minutes before Sarah came over. What were you waiting for?"

"I didn't want the order and I fought to have it removed, but Graham insisted and ten Beckman threatened to use another team. I didn't want anyone to screw it up. I thought if I could just delay long enough something would happen and I wouldn't have to do it, or maybe Sarah would see me and shoot first."

"If she used another team I couldn't stop them, not all of them anyway. Then I would have to tell Walker and she would take him off grid and they would be hunted the rest of their lives."

"I couldn't let that happen to them. Those two have been through enough."

"So you knew she was compromised then?"

"Of course, a piece of drift wood could tell she was compromised! It became clear how far gone she was after your son was thrown off a building."

"Excuse me," Mary said with raised eyebrows.

"I managed to catch him but she didn't know that, she was still on the roof. When I got up there Sarah was fighting a man 7 times her size. She was losing but she just kept going at him. She surprised me that day."

"Why is that," Mary said.

"Because she had an easier way out. The asset was gone and as a spy you are trained when all is lost self-preservation, but she wasn't acting like that. She was fighting as if she had nothing to lose, as if her life didn't matter to her anymore. It was in that moment I knew that he was more important to her then anything else."

"That's why you waited in the apartment," Mary said.

"Yes ma'am. I knew if she saw me that she would stop me from killing Chuck. I knew that she would kill me. Your sons life is worth more then mine, and so is hers," Casey said while looking at the sleeping forms.

"It appears that maybe you are compromised as well Major," Mary said with a slight smile.

"I would agree with you assessment ma'am. With all do respect your son is the biggest pain in the ass that I have ever had, but he brings out the best in me, in all of us," he said while gazing back at Sarah.

"Thank you Major," Mary said.

"For what ma'am?"

"For being honest with me. Lies tend to permeate this business."

"Well ma'am in my experience honor demands honesty and loyalty and your son definitely those qualities."

"Thank you again," she said.

"You are most welcome ma'am."

After a few minutes of silence Casey needed to ask Mary a question.

"Ma'am if I may, could I ask you a favor," he asked.

"Sure Major what is it?"

"The termination order if you could not..,"

"Don't worry I won't tell my son."

"That's great ma'am but could you also not tell Walker," he asked.

"Why John? She will understand once you explain it to her."

"That's just it ma'am I might not get the chance to explain it to her before she goes all Pyscho Sarah on me," he said.

"I think you will be ok," Mary laughed.

"No ma'am I'm serious. She is more then a little protective when it comes to Chuck. She went of grid with him When she thought we had to put him In a bunker. She is going to go ballistic over this," Casey said beseeching her.

"John trust me I will talk to her. Now if you will excuse me I have to go talk to Diane," Mary said as she got up and left.

Casey looked at Sarah wrapped around Chuck and then his gaze followed Mary as she left the room. Who would have thought that this skinny kid would have two of the most dangerous women in the world protecting him, and much worse for any threat, deeply in love with him.

"I hope your mom is right Chuck," Casey said softly.

"Otherwise I better see if there any vacancies at the monastery that Lomax is at."

"God please let Bartowski be able to handle his women," Casey said silently while looking toward the heavens.

It was just after 2 am when the beeping of Chucks heart rate monitor began to increase. Chuck could feel a weight on top of him. It was pressing down on his chest and his upper legs restricting his movement, but his arms felt free. His throat felt scratchy and his eyes were heavy and he felt very warm, almost as if he was wrapped in an electric blanket. His head was a little stuffy, but didn't hurt anymore and his nose was overcome with the odor of vanilla and seemed to tickle a bit every time he exhaled.

He slowly opened his eyes to a tangle of blonde hair propped precariously on his face.

 _Sarah! Of course it was Sarah_ he thought.

He was about to call her name when his ears picked up an interesting sound. It sounded like a dogs squeaky toy slowly being squeezed. It started out as feint but became louder, and it seemed to be coming from Sarah.

Sarah felt the vibration and came awake instantly, she could feel Chuck shaking beneath her. She looked up t his face and saw tears streaming down his face.

"Chuck! Oh God Chuck what's wrong! Chuck talk to me! Oh God Chuck," Sarah cried as she grabbed his face in her hands.

"Shhshhar," Chuck slurred.

"Chuck I'm here! I'm right here! Talk to me Chuck! Please baby I'm right here tell me what's wrong," Sarah cried through tears.

"Sarrrah….Sarah…your….snoring," Chuck laughed.

"I'm what? What Chuck," she answered with concern.

"You're snoring….really loud," he laughed.

"You son of a bitch! I thought you were having a seizure. Do you have any idea how worried I have been you son of a bii…," was as far as she got when Chuck pulled her down for a kiss.

Sarah immediately surrendered when his lips found hers. All of her fears, stress, and emotional pain over the last few days evaporated in mere seconds.

Regrettably the need for air required Chuck to break the kiss, and as he broke the kiss he smiled at Sarah's still tear stained face.

"Thank you Sarah," Chuck said.

"For what," she said as she looked steadily at him.

"For saving my life, for being my life. I don't know what would happen to me if I didn't have you. I love you," he said.

Sarah immediately reinitiated the kiss.

"I love you too Chuck, I was so scared. So scared that I lost you. I couldn't survive if that happened," she said as she laid her head on his chest.

"I'm sorry Sarah. I know, but I'm here now," he said while striking her hair.

"Chuck I need to tell you something," she said.

"What is it baby...owww Sarah..."

In an instant she had his hands pinned up behind his head and straddled him, bringing her face centimeters from his.

Her eyes flashed cold blue as she looked into his.

"IF YOU Ever! Ever! Ever! Scare me like this again I will turn you into a eunuch! Is that clear!"

"Oh c'mon Sarah don't you think you are being...ouch Christ Sarah!"

"Is that clear!"

"Yes! Yes! Jesus Christ Yes," he said as she finally released his wrists.

"Good. Now come here," she said as she snuggled back up against him.

"I love you Sarah," Chuck said as he began to doze off.

"I love you too Chuck. More then you will ever know," she replied groggily.


	17. Chapter 17

_A/N: Hello all we have come to the end of the story. I want to thank everyone for their kind words and tips. As this is my first fanfiction I really didn't know what to expect, but was blown away by all the support. Depending on reader interest I might continue this series and have a few others ideas as well...anyway thanks again and on with the story...As usual I don't own chuck nor make any $ from it and sadly I doubt there will ever be a movie..._

Mary was sitting quietly in a side bank of chairs outside of the conference room waiting to speak with the general. Beckman was talking with Casey, and although she was not really listening, she knew it had to do with dispatching former director Lomax.

After a few minutes Casey came out carrying a file folder and caught Mary's eye.

"Hello ma'am," Casey said as he stopped briefly to talk with her.

"Hello Major. I trust you are doing well," Mary replied.

"Very well ma'am. I heard Chuck has woken up. How is he doing?"

"I'm not sure major. I actually haven't gone to see him yet."

"I beg your pardon ma'am, but why," Casey asked.

"It's complicated Major."

"It always is when it comes to Chuck," Casey replied.

"What was that Major," Mary asked while she tried unsuccessfully to hide her agitation.

"I'm sorry ma'am."

" No Major say what you need to say," Mary said.

"Ma'am I have been a soldier most of my life, and I have been a spy for more then half of it. You look to me like you are ready to leave."

"You're very observant Major."

"So you are just going to leave? Not looking forward to a family reunion," Casey asked sarcastically.

"You should not pay attention to things that don't concern you Major," Mary said while giving him hard eyes.

"If it concerns the welfare of my team then it concerns me," Casey said meeting her eyes.

Casey looked into her eyes and saw the pain. Years of hard trials have taken their toll. He saw her sadness, fear, and her self-loathing, and he knew exactly what she feeling.

"What do you want Major," Mary asked.

"I know how you are feeling ma'am, I think you should reconsider your plans," Casey said.

"I don't think that is any concern of yours," Mary said dismissively.

"Ma'am as I said if it concerns my team then it concerns me. Your son has been through the ringer the last few years. You suddenly come back into his life and now you are leaving. How do you think that will make him feel," Casey asked.

"I need to leave to keep him safe!"

"Oh bullshit! You are afraid!"

"Afraid of what!"

"Afraid of what he thinks of you! "

"You have no idea what you ..,"

"I know exactly what I'm talking about! Your son knows everything I have ever done for this country! Every terrible thing I was ever ordered to do. He has been betrayed by so many people who have been so close to him, and yet he still believes in people."

"Is that so Major? Tell me did you ever tell him that you were assigned to kill him," Mary asked with scorn.

Casey looked at her for a hard second, and then completely shocked her.

"Yes I did Ma'am. I was ready to quit this team and to resign my commission, but do you want to know why I am still here?"

"Why Major?"

"Because of your son! He asked me to stay, even after I told him everything and was sure that he would never trust me again. I told him that I would never again betray him, but I was sure he would never believe me. After I gave him every reason not to, your son still believed in me and he made me a better soldier and man for it."

" What are you saying Major?"

"I'm saying your son is special, it's almost like he takes defective people and fixes them. Me, Walker, even you, your son still believes in you," Casey said.

Mary knew that Casey hit it right on the head. Never before had someone put it so clearly to her. She was afraid of how her son would see her, and was sure that he would never forgive her.

"The situation is just too difficult, it been too long," Mary replied while a few tears escaped her eyes.

"No ma'am the situation isn't difficult , we make it difficult because we're spies.. Chuck is easy, he forgives people who hurt him. I promise you that he will understand, but you already know that, don't you Mary," Casey asked.

Casey looked at her and could see her resolve weakening, but he knew that he could not force her.

"If you will excuse me ma'am I have some business to attend to," he said as he walked away leaving her to decide.

A few hours later Chuck had managed to convince Sarah to go home and rest up for a while, and was just about to attempt some type of food that was designated eggs by the hospital cafeteria, when he heard a knock on his door.

"Hi Chuck. How are you feeling," Mary asked while standing in the doorway.

"Hi mom. I'm doing ok. A little tired but not too bad. Want to come in," he asked motioning to an empty chair.

"Only if I'm not bothering you, or interrupting you and Sarah," Mary replied sheepishly as she tentatively entered the room.

"Oh no it's no bother, and I finally got Sarah to go home for a while," he said.

"How did you manage that? That girl is particularly fond of you and a little, how shall I say, fanatically protective of you," Mary said.

"Ha yeah she is. some would say maybe a bit crazy, but it's a good kind of crazy," he replied chuckling.

"Yes I suppose. Your other team member John Casey seems to be afraid of her," Mary laughed.

"Really? Casey Ha! Oh wait till I tell him," Chuck laughed.

They came to the first uncomfortable silence of the conversation and Mary dreaded what to say next. She wanted to explain everything to Chuck, but she didn't really know where to begin and it was making her very frustrated.

"Mom would you mind if we took a walk? I have been in bed for so long I just want to get moving a bit."

"Sure, but are you sure that you can handle it?"

"Oh yeah. When the doctor came by he said it would be good for me in moderation. Of course when Sarah was here she wouldn't let me," Chuck laughed.

"Well she is just being cautious," Mary said as she helped him up.

"Yeah like a grizzly bear," Chuck quipped as she got to his feet.

"Now don't push yourself to hard Chuck," Mary said as he leaned into her for support.

"I won't

They made their way down the hall and Chuck was a little sore after a while, so they made their way down to the atrium at the center of the hospital. Given that this was secure floor, Alfa team was within sight, but they kept a safe distance giving Chuck and his mom privacy to talk.

They both had urgent things to say and were noticeably anxious.

"Chuck I want to apologize for.."

"Mom if I could go first I really need to tell you something," Chuck said.

"Ok sure, go ahead," She said.

"Mom when I was in my little slumber here, I had access to a few files that Dad had put in the intersect specifically for me. They were about our family, mostly about how we ended up where we are and what you did for the CIA."

 _Oh God he knows...he must have seen my mission files..he knows I'm a monster..._ she thought.

"Chuck listen I...,"

"I will never be able to thank you enough for what you did for our family. I am sorry for not understanding," he said.

"For not understanding what," Mary said as she felt the tears coming.

"I was mad at you for so long. I felt that you abandoned us. I am so sorry for that. I could not understand how you could do what you did, until I...," Chuck stumbled as emotion overcame him.

"Until you fell in love with a spy," Mary said through her tears.

"Yeah," he replied.

"She's the one isn't she Chuck," Mary said.

"Yeah she is. I can't imagine my life…. I don't want to imagine my life without her."

"But Mom you know what this life can do to people. I mean you and Dad, what you had to do to...,"

"What I had to do was worth it. Your Father was the best thing to ever happened to me, until you and your sister came along," Mary said as she clutched her charm necklace.

"Your was the first really true thing in my life, and he saved me by giving me the love that I needed. I was a very bad person before I met your father, I had no home or family and I was hollow inside. I had nothing in my soul but pain and the government used that to make me a killer."

"Mom you are not…,"

"Yes I am Chuck. At least I was until I met your father. I never loved anyone or anything until him. When you and your sister were born life took on a whole new meaning."

"What do you mean?"

"Chuck the only thing that I love in this world is my family. That is all that matters to me. My life never really began until I met your father and you and your sister will always be the greatest things I have ever done for this world. After years of pain and sadness my heart was finally filled with love and its that which defines me now."

"What I am saying Chuck is that my family is my home, and the only way I could keep it safe was to do what I did," Mary said as the tears came again.

"I'm so sorry…I never wanted to leave you but I….,,"

Thant was as far as she got before Chuck embraced his mother. The two held each other for a few minutes just sobbing silently and reuniting.

"Mom why don't you come home?"

They made their way back towards Chuck's room and from the end of the corridor, saw a refreshed Sarah Walker waiting for them. Chuck's face lit up like a Christmas tree when he saw her, and hers returned the voltage.

"Excuse me Chuck, but I need a word with your mother," Beckman said as she appeared next to Mary.

"You go Chuck, I'll be along in a little while," Mary said as Chuck turned and walked toward Sarah.

"So Mary have you thought about my offer," Beckman said as they watched him head down the corridor.

"Yes Diane. I would like to come in and put in my papers," Mary replied.

"Good. I'm sure we can move up your pension a bit due to your service," Beckman replied.

"I have to go to Boston first. I want to see Ellie," Mary said.

"I thought you might. I have the plane at your disposal. Well I'll be in the conference room when your ready," Beckman said as she left her in the hallway.

When Beckman got back to the conference room she sat down and pulled an old weathered photograph out of her wallet. The picture showed a young couple with their toddler daughter and infant son. It was taken in the hospital as the woman was still in bed holding the infant and the man had a hold of the toddler. She flipped the picture over to read the inscription.

 _Diane,_

 _We can't thank you enough for everything you have done for us. Please say hello to our new son Charles! Mary is perfect after delivery, and Ellie and I are excited with our new addition. We are hoping you would consider being his Godmother?_

 _Thanks again and all of our love to you_

 _Steve_

"Son of a bitch," Beckman softly said as a tear escaped her eye.

Mary looked at the scene before her and her mind drifted back to that day all those years ago when her life changed forever….

The blonde agent approached the mark and made her way to the desk. Her mark had his head down after being exhausted by people with computer issues, and didn't see her as she approached and rang the bell.

"Oh not another one," he said as he looked up at her through tired eyes.

His brown eyes found her blues and in an instant they both froze, as they both began to have a strange feeling. It was like being very excited, but also calm at the same time.

 _Oh my God….Who is this woman…she is so beautiful…why am I feeling like this._ He thought.

 _Control…you have done this a million times…there is nothing special about him…focus…why am I nervous_ …she thought.

"Ha..Hi..Hi..can I help you with something," he stammered.

She couldn't suppress the smile that spread across her lips, and when he returned one she felt like he could see right through her.

"Oh yes I'm having an issue with my computer," she said.

"Oh no problem, that's why I'm here. Everybody is getting into the new personal computer craze," he replied laughing.

"My name is Steve. And you are," he asked while extending his hand.

Name…my name…what name do I use…Sarah…that's it…Sarah…she thought.

"I'm…Sa...rr…ah Mary," she said as she clasped his hand.

"Did you say Mary," he asked while smiling.

"Yes Mary," she said as she returned his smile.

"Nice to meet you Mary. What can I do for you?"

As she watched Sarah embrace Chuck and lead him back into his hospital room she wiped a tear from her eye and spoke softly to herself.

"He is his fathers son."


End file.
